ABSTRACT Candida albicans is a common fungal commensal and opportunistic pathogen occupying the skin, oral cavity, gastrointestinal tract, and genitourinary tract of its human host. Overgrowth of C. albicans within these host niches can lead to mucosal and systemic disease and typically relies on pathogenic processes such as the yeast-hyphal transition. Hyphae are capable of breaching host mucosal barriers through active penetration and endocytic uptake that both lead to host cell destruction and transmigration of C. albicans to deeper tissues. Thus, host epithelial cells serve a vital role in detecting C. albicans overgrowth and signaling to professional phagocytes to remove invasive fungal cells. Interestingly, natural C. albicans isolates obtained from clinical setting display a range of filamentation phenotypes, including strains unable to produce hyphae. Here, we will investigate the genetic determinants underlying natural occurring phenotypic variation in C. albicans that regulates the ability to filament and/or colonize the oral cavity through the first use of quantitative genetic approaches in C. albicans. A genetically diverse set of sequenced clinical C. albicans isolates forms the basis of this study as they display significant variation in filamentation processes in vitro and the ability to cause disease in vivo. First, gene expression across the sequenced isolates will facilitate construction of co- expression network modules that associate with in vitro filamentation phenotypes. Expression of key transcriptional regulators within each predicted module will be tested in multiple strain backgrounds for altered in vitro filamentation across a variety of solid and liquid substrates. Automated phenotyping of filamentation, adhesion, and invasion of agar substrates will be built to facilitate scoring mutant phenotypes (Aim 1). In Aim 2, quantitative trait loci (QTL) mapping will be developed utilizing the parasexual program, an alternative mating and ploidy reduction system in C. albicans, to identify the genes responsible for differences in filamentation and epithelial damage between C. albicans strains incubated with OKF6/TERT-2 oral epithelial cells. Identified genes that modulate filamentation and epithelial damage in tissue culture systems will be subsequently tested for in vivo colonization and filamentation phenotypes of a murine model of oropharyngeal candidiasis. Preliminary experiments suggest that filamentation and damage of oral epithelial cells are separable phenotype, which will be explored further through dual-species RNA sequencing of strains separated by filamentation (+/-) and cell damage (+/-) phenotypes incubated with OKF6/TERT-2 cells (Aim 3). This Aim will also determine the role of recently identified host genes with differential expression between damaging and colonizing strains in host cell signaling and transcriptional responses that lead to either filamentation or host cell damage during interaction with oral epithelial cells. Together, these studies will determine the pathways and processes modulated by genetic diversity in C. albicans that lead to divergent filamentation and epithelial damage phenotypes that contribute to commensalism v. disease.